The Symplegma project, a java computational ...

The Symplegma project

Symplegma Introduction Options and choices

The Symplegma project, a java computational mechanics framework.

SDE Description

Java code

Christos G. Panagiotopoulos

jFEM jBEM FuturEye PDE Climax GEN

Conclusions

29-09-2016 Technical University of Crete School of Production Engineering & Management




SDE Description

Java code

What is Symplegma?


Conclusions


Symplegma: a computational mechanics framework and beyond The Symplegma project


SDE Description

Java code jFEM jBEM FuturEye PDE Climax GEN

Conclusions

• An effort of a coordinated utilization of, several years,

experience and work have been done using java for implementation of computational mechanics methods. • Initiated in 2008 at AUTh, further developed mainly at

UoS and at CUP, while the current form is given during a stay at FORTH. • Main orientation of the project and the respective software

is education and research.


Computational mechanics and numerical computing The Symplegma project

From International Association for Computational Mechanics website Symplegma Introduction Options and choices

SDE Description

Computational Mechanics (CM) is the development and application of numerical methods and digital computers to the solution of problems posed by Engineering and Applied Science with the objectives of understanding and harnessing the resources of nature.


Conclusions

Interdisciplinary CM involves different fields of expertise. Its three pillars are mathematics, computer science, and mechanics. Computational fluid dynamics, computational thermodynamics, computational electromagnetics, computational solid mechanics are some of the many specializations within CM.


Numerical methods The Symplegma project


SDE Description


Conclusions

Mathematics Ordinary and Partial differential equations, linear algebra and numerical analysis. Methods FEM, FDM, and BEM are the most popular numerical methods used in order of dominance. In solid mechanics FEM are far more prevalent, whereas in fluid mechanics, thermodynamics, and electromagnetism, FDM are almost equally applicable. The BEM is in general less popular, but has a niche in certain areas (e.g., acoustics, fracture).


Recent publications on numerical computing The Symplegma project

Some recently published booka on numerical modelling and scientific calculations. 1. G.E. Stavroulakis, M.E. Stavroulaki & A.D. Muradova (2015) Computational Mechanics, HEAL-Link∗ (in greek)


2. M. Plexousakis & P. Chatzipantelidis (2015) Numerical solution of partial differential equations, HEAL-Link∗ (in greek)

SDE

3. T. Hatzigogos & F. Karaoulanis (2015) Finite element method for geotechnical mechanics, HEAL-Link∗ (in greek)

Description


4. J.T. Katsikadelis (2016) The Boundary Element Method for Engineers and Scientists: Theory and applications, Academic Press, Elsevier

Conclusions

5. H.P. Langtangen, S. Linge (2016) Finite Difference Computing with Partial Differential Equations∗ 6. H.P. Langtangen, K.A. Mardal (2016) Introduction to Numerical Methods for Variational Problems∗ ∗

Released under Creative Commons license The Symplegma project

Java? The Symplegma project

General Java is a general purpose, computer programming language, gained


SDE Description


Conclusions

widespread popularity. Appealing features of Java include: clean and simple syntax, high level of maintainability of Java code, portability, automatic memory management, multithreading and networking capabilities, wealth of libraries and tools.

Science Early interest in Java from the scientific communities to determine the level of performance offered by Java, and its suitability for developing scientific software. The Java Grande Forum (JGF) was an initiative to encourage interest in Java amongst the scientific and HPC communities.


Java for numerics? The Symplegma project


SDE Description


Conclusions

• JScience: Java tools and libraries for the advancement of

sciences. • JAS: Java Algebra System Project. • SymJava: A Java library for fast symbolic-numeric

computation. • GeoGebra: an interactive geometry, algebra, statistics and

calculus application, intended for learning and teaching mathematics and science. • jLab: Scientific Scripting for the Java Platform. • Gaia: An efficient framework for Java data processing

systems in HPC environments. . . . to mention but a few . . . The Symplegma project

The Symplegma components The Symplegma project


• Java code/libraries of numerical methods. • An integrated yet simple graphical environment called SDE

(Symplegma Development Environment).

SDE Description

Java code

• A domain specific language (DSL)1 to be used as the

interpreter’s language which we call Climax.


Conclusions

1

Well known DSLs, in the context of mathematics, could be considered the Matlab and Mathematica. Another example is the UFL (Unified Form Language) of the FEniCS Project, a domain specific language for declaration of finite element discretizations of variational forms. The Symplegma project

Why and for what reason? The Symplegma project


SDE Description


Conclusions

Java We consider Java as an alternative, and not subsitute, language for numerical, scientific and engineering computations. Still FORTRAN, C and C++ are the dominants together with Python playing a crucial role in the field. Java should be considered both for the language and the Java Virtual Machine, while lot of significant languages running on the JVM have been arised (e.g. Groovy, Scala, Clojure, Jython, JRuby, etc.). Symplegma & SDE Symplegma and the respective platform SDE are considered to become an integrated computational mechanics platform with main orientation research and education. Substitution of commercial or open source code capable to handle huge problems of industry is not considered. The Symplegma project

Compiled or Interpreted implementation? The Symplegma project

Compilation In a compiled implementation of a language, a compiler translates the source code directly into code that is specific to the target machine (machine code) specific to a given processor and operating system. Then the


SDE Description


computer will run the machine code on its own.

Interpretation In an interpreted implementation of a language, the source code is not directly run by the target machine. What happens instead is that another program reads and then executes the original source code. This other program is also known as the interpreter. The interpreter is usually written specifically for the native machine.

Conclusions

Symplegma implementation? Symplegma, following java (and/or groovy), is compiled into Java bytecode to be interpreted or compiled by JVM. The Java bytecode can be used in any processor and operating system assuming that it is eqquiped with some JVM. A JIT compiler (part of JVM) may compile the bytecode into native machine code (faster) at runtime, applying sophisticated optimization techniques. The Symplegma project

Programming or Scripting mode? The Symplegma project

Programming In computer software, a general-purpose programming language is a programming language designed to be


SDE Description


Conclusions

used for writing software in a wide variety of application domains (a general-purpose language).

Scripting A computer script is a list of commands that are executed by a certain program or scripting engine in order to achieve a specific goal. Scripting could be seen as programming at a high and flexible abstraction level.

Symplegma mode? We may consider the SDE platform as a general purpose program in order to produce both scripts, taking advantage of Groovy or BeanShell (etc.), and integrated applications, taking advantage of Java itself, both of these modes together with predefined code unified in Climax .


Web or Standalone application? The Symplegma project

Standalone application Not being experts in IT, we define here the standalone or desktop application as any software that can be


SDE Description


Conclusions

installed on a single computer (laptop or a desktop) and used to perform specific tasks.

Web based application Opposing the above definition for desktop applications, we consider (again in a simplified manner) web based applications those for which by some means Internet connectivity is necessary.

Symplegma application? SDE platform could be considered both as a desktop application and web based one through the technology of Java Web Start. Using Java Web Start technology, standalone Java software applications can be deployed with a single click over the network. Java Web Start ensures the most current version of the application will be deployed, as well as the correct version of the Java Runtime Environment (JRE, the software package that contains what is required to

run

a Java program).


Proprietary or Open source software? The Symplegma project

Proprietary Proprietary software is computer software for which the software’s publisher or another person retains


SDE Description


Conclusions

intellectual property rightsusually copyright of the source code, but sometimes patent rights.

Open-source Open-source software (OSS) is computer software with its source code made available with a license in which the copyright holder provides the rights to study, change, and distribute the software to anyone and for any purpose. Open-source software may be developed in a collaborative public manner.

Symplegma license? Software freedom plays a fundamental role in education. With the aim of increasing collaboration and communication within the scientific computing community we have adopted the open-source model for the Symplegma development using an appropriate license (e.g. GNU, Creative Commons, etc).




SDE Description


SDE: An integrated development environment for Symplegma components

Conclusions


Description of SDE environment The Symplegma project


SDE Description


Conclusions

The (a) (b) (c)

SDE environment consists of three segments the text area (input) the communication area (output) the area of graphical visualization (output) The Symplegma project

SDE text area The Symplegma project

The input text area is a tabbed text editor and file viewer. Symplegma Introduction Options and choices

SDE Description


Conclusions

• syntax highlight • auto suggetions and completion • commentization • input command interaction

Regarding the latter, text in these areas could be used as input commands or scripts passed to the BeanShell or GroovyShell interpreter. The result of execution of these commands/scripts interacts with the communication text area and/or the visualization area (Graphics panel).


SDE communication area The Symplegma project


SDE Description


Conclusions

The communication area is where the program communicates unidirectionally with the user. It is a tabbed area of four fixed tabs as its components. All these four tabs are ASCII textual viewers. • Output tab which actually is the output stream for the

program. • Console tab shows the numbered commands that have

been passed to and executed by the interpreter. • Errors tab is the errors/warnings output stream • Comments area consists of simple messages or comments

that the program sends to the user.


SDE area of graphical visualization The Symplegma project


SDE Description


Conclusions

A two dimensional (2D) visualization area has been implemented using java graphics for the swing components. Three dimensional (3D) is a future plan possibly developed by utilization of java3d or jogl (java openGL) libraries. Graphics panel is interactive with some standard operations: • standard transformations (translation, zoom) • choice of colours, etc. • goemetry display • at rest results display • animation of results




SDE Description


The java source code, classes and libraries

Conclusions


Java implementation of computational mechanics The Symplegma project


Besides pure Java, Symplegma includes the java code of computational mechanics implementation, already existed, or under development. • Finite element method of engineering approach using

jFEM, a java implementation have been developed.

SDE Description


Conclusions

• Boundary element method of engineering approach using

jBEM, a java implementation have been developed. • FEM numerical solution of PDEs utilizing FuturEye2 • A general domain specification for user defined approaches

of direct interaction with SDE components. 2

Still on a trial basis for SDE compatibility. Developed by Prof. Yueming Liu, Department of Mathematics, University of Texas at Arlington, USA. The Symplegma project

The code skeleton The Symplegma project


SDE Description


Conclusions

Pre-processing

Processing

• Declare variables

• Declare algorithms

• Define domains

• Set analysis’ parameters

• Define nodes

• Do the analysis

• Define element • Define other necessary

entities

Post-processing • Manipulating results • Visualize • Plotting




SDE Description


jFEM: The finite element method implementation

Conclusions


FEM “Hello world” and its code The Symplegma project


SDE Description

Java code

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

jFEM jBEM FuturEye PDE 16 Climax GEN 17

Conclusions

18 19 20 21 22 23 24 25 26 27

# fem ” H e l l o w o r l d ” l i k e import jfem . ∗ ; // a s k t h e u n i v e r s e t o p r o v i d e a domain aDomain=t h e U n i v e r s e . FEMDomain ( ) ; // d e f i n e a node and add i t i n t o t h e domain aNode= new Node ( 1 , 0 . 0 ) ; aDomain . putNode ( aNode ) ; // d e f i n e some m a t e r i a l aMate r = new E l a s t i c M a t e r i a l ( 1 , 1 0 0 0 . 0 ) ; aDomain . p u t M a t e r i a l ( aMate r ) ; // d e f i n e a c r o s s s e c t i o n ( t h e a r e a o f t h a t one d o f e l e m e n t ) a C r o s s S e c t i o n = new C r o s s S e c t i o n ( 1 , 1 . 0 ) ; aDomain . p u t C r o s s S e c t i o n ( a C r o s s S e c t i o n ) ; // d e f i n e some e l e m e n t and t h e n put i t i n t h e domain anElem = new OneDOF ( 1 , aDomain . ge tNode ( 1 ) , aDomain . g e t M a t e r i a l ( 1 ) , aDomain . g e t C r o s s S e c t i o n ( 1 ) , 1) ; aDomain . p u t E l e m e n t ( anElem ) ; // c o n s t r u c t some l o a d s and a l o a d c a s e aL oadC ase = new L oadC ase ( 1 ) ; aL oadC ase . putL oad ( new Load ( 1 0 0 . 0 , 1 , 1) ) ; aDomain . putL oadC ase ( aL oadC ase ) ; // d e f i n e t h e a n a l y s i s t h a t w i l l manage p r o b l e m ’ s s o l u t i o n t h e A n a l y s i s = new S t a t i c A n a l y s i s ( aDomain ) ; // now we may a s k t h e A n a l y s i s t o a n a l y s e . . . t heA n a ly sis . analyse (1) ; theAnalysis . endAnalysis () ; // // d e f o r m a t i o n theGP . p l o t D e f o r m ( 1 , 0 . 5 , 1) The Symplegma project

FEM “Hello world” and its code The Symplegma project


SDE Description


Conclusions


A simple truss example3 The Symplegma project

Symplegma

• Modulus of elasticity

Introduction Options and choices

E=2.1×108 kN/m2

SDE

• Section area A=0.001m

Description

• Force F =70N


Conclusions

3

Example taken from Stavroulakis, Stavroulaki & Muradova, Computational Mechanics, HEAL-link, (sec. 3.6.1) The Symplegma project

A simple truss example 1 2 3 4 5 6 Symplegma 7 8 Introduction 9 Options and choices 10 11 SDE 12 Description 13 14 Java code 15 jFEM 16 jBEM FuturEye PDE 17 18 Climax GEN The Symplegma project

Conclusions

19 20 21 22 23

import jfem .∗ aDomain=t h e U n i v e r s e . FEMDomain ( ) // d e f i n e t h e n o d e s aDomain . putNode ( new aDomain . putNode ( new aDomain . putNode ( new aDomain . putNode ( new

Node ( 1 Node ( 2 Node ( 3 Node ( 4

,0.0 ,0.0) ) ,1.5 ,0.0) ) ,1.5 ,0.866) ) ,0.0 ,0.866) )

// d e f i n e m a t e r i a l aDomain . p u t M a t e r i a l ( new E l a s t i c M a t e r i a l ( 1 , 2 . 1 ∗ 1 0 8 . 0 ∗ 1 0 0 0 . 0 ) ) ; // d e f i n e C r o s s S e c t i o n s aDomain . p u t C r o s s S e c t i o n ( new C r o s s S e c t i o n ( 1 , 0 . 0 0 1 ) ) ; // d e f i n e e l e m e n t s aDomain . p u t E l e m e n t ( new T r u s s 2 d ( 1 , aDomain . ge tNode ( 1 ) , aDomain . ge tNode ( 2 ) aDomain . g e t M a t e r i a l ( 1 ) , aDomain . g e t C r o s s S e c t i o n ( 1 ) ) ) aDomain . p u t E l e m e n t ( new T r u s s 2 d ( 2 , aDomain . ge tNode ( 2 ) , aDomain . ge tNode ( 3 ) aDomain . g e t M a t e r i a l ( 1 ) , aDomain . g e t C r o s s S e c t i o n ( 1 ) ) ) aDomain . p u t E l e m e n t ( new T r u s s 2 d ( 3 , aDomain . ge tNode ( 4 ) , aDomain . ge tNode ( 3 ) aDomain . g e t M a t e r i a l ( 1 ) , aDomain . g e t C r o s s S e c t i o n ( 1 ) ) ) aDomain . p u t E l e m e n t ( new T r u s s 2 d ( 4 , aDomain . ge tNode ( 1 ) , aDomain . ge tNode ( 4 ) aDomain . g e t M a t e r i a l ( 1 ) , aDomain . g e t C r o s s S e c t i o n ( 1 ) ) ) aDomain . p u t E l e m e n t ( new T r u s s 2 d ( 5 , aDomain . ge tNode ( 1 ) , aDomain . ge tNode ( 3 ) aDomain . g e t M a t e r i a l ( 1 ) , aDomain . g e t C r o s s S e c t i o n ( 1 ) ) ) aDomain . p u t E l e m e n t ( new T r u s s 2 d ( 6 , aDomain . ge tNode ( 4 ) , aDomain . ge tNode ( 2 ) aDomain . g e t M a t e r i a l ( 1 ) , aDomain . g e t C r o s s S e c t i o n ( 1 ) ) ) The Symplegma project

, , , , , ,

A simple truss example The Symplegma project

24 25 26 27 28 29 Symplegma 30 Introduction 31 Options and choices 32 33 SDE 34 Description 35 36 Java code 37 jFEM 38 jBEM FuturEye PDE 39 40 Climax GEN 41 Conclusions 42 43 44 45 46 47 48 49

// c o n s t r u c t some l o a d s Load aLoad ; L oadC ase aL oadC ase ; aL oadC ase = new L oadC ase ( 1 ) ; aLoad =new Load ( − 70 , 2 , 2) ; aL oadC ase . putL oad ( aLoad ) ; // put L oadC ase t o domain aDomain . putL oadC ase ( aL oadC ase ) ; // b o u n d a r y c o n d i t i o n s d o u b l e Ak=10.0 e 16 ; ConstraintElement aConstraintElement ; i n t i d =0; f o r ( i n t i =1; i

The Symplegma project, a java computational ...

The Symplegma project, a java computational ...

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